BioImageAnalysisNotebooks

BioImageAnalysisNotebooks copied to clipboard

Hi Robert @haesleinhuepf, This is a PR that proposes a large reorganisation of the chapter 12. The initial goal was just to better explain the role of Numpy but as...

guiwitz

Few fixes in napari notebook: - The magic command for qt is not needed anymore. - No colormap was actually used as said in the text - The viewer screenshots...

guiwitz

General questions

2

I went a bit through the (great!) material and before trying to improve here and there, I have a few questions: - Is there anywhere a plan of the entire...

guiwitz

napari and nD visualization

1

The chapter "Image visualization in 3D" actually presents nD visualization cases rather than just 3D. Should it be renamed? Also the [notebook on napari](https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/16_3d_image_visualization/05_napari.html) only uses the blobs image and...

guiwitz

Intro questions

3

Hi @haesleinhuepf, I have been looking through the introductory part and have a few questions. I don't want to create a separate issue for each of them or make a...

guiwitz

Issue on page /12_image_analysis_basics/02_Working_with_images.html - data

2

Hey @haesleinhuepf, working through the section "12_image_analysis_basics/02_Working_with_images" I found the "blobs.tif" using Fiji, but I am not sure where I would find the dataset "banana020.tif" for the exercise? Have I...

ElisabethKugler

... for now I'm just creating PR draft to not forget about this :-D

haesleinhuepf

Matplotlib Image Figures

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Hi Robert, Super cool collection of notebooks! One of my tasks is to teach users about bio-image analysis and I am in awe of the beauty of this collection. Thanks...

tibuch

contributions

4

What an amazing resource @haesleinhuepf ! I had in mind to extend some of my courses in this way but of course never found time. I'm planning a workshop on...

guiwitz

fix F1 score computation

1

Partially? close https://github.com/haesleinhuepf/BioImageAnalysisNotebooks/issues/27 Hello, I hope you are going well. This PR proposes to update : - The distance matrix label plot to make it more self-explanatory - The `compute_true_positives`...

ClementCaporal